rs1478224

chr4-167515850-C-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.576 in 151,836 control chromosomes in the GnomAD database, including 25,222 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (25222 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87362 AN: 151718 Hom.: 25212 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.550

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.576 AC: 87406 AN: 151836 Hom.: 25222 Cov.: 31 AF XY: 0.572 AC XY: 42449 AN XY: 74160

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.551

Alfa AF: 0.596 Hom.: 11740

Bravo AF: 0.571

Asia WGS AF: 0.537 AC: 1862 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
Cadd	Benign	14
Dann	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1478224; hg19: chr4-168437001;